X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_fastq;h=eb926618efdeae2dff7bd5ddc50fab0fd1771b43;hb=b0b818d9a5cd88c597d99afbc102dfbbf8782f94;hp=df2ad6e088d786fa12bce015627d0ce89a3a250e;hpb=e6d927577f0e4b46ccd4f978f6c5dcbf334c25aa;p=biopieces.git

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index df2ad6e..eb92661 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -42,8 +42,9 @@ $options = Maasha::Biopieces::parse_options(
     [
         { long => 'data_in',     short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
         { long => 'num',         short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => 0     },
-        { long => 'quality',     short => 'q', type => 'uint',   mandatory => 'no', default => 20,    allowed => undef, disallowed => undef },
-        { long => 'skip_scores', short => 's', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'convert2dec', short => 'c', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'cutoff',      short => 'C', type => 'int',    mandatory => 'no', default => 20,    allowed => undef, disallowed => undef },
+        { long => 'soft_mask',   short => 's', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -64,13 +65,8 @@ if ( $options->{ 'data_in' } )
     {
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
-            if ( not $options->{ 'skip_scores' } )
-            {
-                Maasha::Fastq::lowercase_low_scores( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'quality' } );
-
-                $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
-                $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
-            }
+            Maasha::Fastq::softmask_phred_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
+            $record->{ 'SCORES' } = Maasha::Fastq::phred_str2dec_str( $record->{ 'SCORES' } ) if $options->{ 'convert2dec' };
 
             Maasha::Biopieces::put_record( $record, $out );
         }